DNA Barcoding For Species Identification Research Articles

DNA Barcoding for Species Identification of Moss-Dwelling Invertebrates: Performance of Nanopore Sequencing and Coverage in Reference Database

In view of the current biodiversity crisis and our need to preserve and improve ecosystem functioning, efficient means for characterizing and monitoring biodiversity are required. DNA barcoding, especially when coupled with new sequencing technologies, is a promising method that can, in principle, also be employed by taxonomic lay people. In this study we compare the performance of DNA barcoding by means of a third-generation sequencing technology, nanopore sequencing with classical Sanger sequencing, based on a sample of invertebrates collected from moss pads in a bog in Austria. We find that our nanopore sequencing pipeline generates DNA barcodes that are at least as good as barcodes generated with Sanger sequencing, with the MinION producing better results than the Flongle flowcell. We further find that while many arthropod taxa are well covered in the international reference DNA barcode database BOLD, this clearly is not the case for important taxa like mites and springtails, which hampers large-scale biodiversity assessments. Based on examples from our study we further highlight which factors might be responsible for ambiguous species identification based on BOLD and how this can, at least partly, be solved.

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

BackgroundThe genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, the evolutionary history of this genus also remains inadequately understood. The plastid genomes possessing highly conserved structure and limited evolutionary rate have proved to be an effective tool for studying plant phylogeny and evolution.ResultsIn the current study, we newly sequenced and assembled fifteen Sanicula complete plastomes. Combined with two previously reported plastomes, we performed comprehensively plastid phylogenomics analyses to gain novel insights into the evolutionary history of this genus. The comparative results indicated that the seventeen plastomes exhibited a high degree of conservation and similarity in terms of their structure, size, GC content, gene order, IR borders, codon bias patterns and SSRs profiles. Such as all of them displayed a typical quadripartite structure, including a large single copy region (LSC: 85,074–86,197 bp), a small single copy region (SSC: 17,047–17,132 bp) separated by a pair of inverted repeat regions (IRs: 26,176–26,334 bp). And the seventeen plastomes had similar IR boundaries and the adjacent genes were identical. The rps19 gene was located at the junction of the LSC/IRa, the IRa/SSC junction region was located between the trnN gene and ndhF gene, the ycf1 gene appeared in the SSC/IRb junction and the IRb/LSC boundary was located between rpl12 gene and trnH gene. Twelve specific mutation hotspots (atpF, cemA, accD, rpl22, rbcL, matK, ycf1, trnH-psbA, ycf4-cemA, rbcL-accD, trnE-trnT and trnG-trnR) were identified that can serve as potential DNA barcodes for species identification within the genus Sanicula. Furthermore, the plastomes data and Internal Transcribed Spacer (ITS) sequences were performed to reconstruct the phylogeny of Sanicula. Although the tree topologies of them were incongruent, both provided strong evidence supporting the monophyly of Saniculoideae and Apioideae. In addition, the sister groups between Saniculoideae and Apioideae were strongly suggested. The Sanicula species involved in this study were clustered into a clade, and the Eryngium species were also clustered together. However, it was clearly observed that the sections of Sanicula involved in the current study were not respectively recovered as monophyletic group. Molecular dating analysis explored that the origin of this genus was occurred during the late Eocene period, approximately 37.84 Ma (95% HPD: 20.33–52.21 Ma) years ago and the diversification of the genus was occurred in early Miocene 18.38 Ma (95% HPD: 10.68–25.28 Ma).ConclusionThe plastome-based tree and ITS-based tree generated incongruences, which may be attributed to the event of hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture. Our study highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions, and to efficiently explore the evolutionary history of this genus. Molecular dating analysis explored that the diversification of the genus occurred in the early Miocene, which was largely influenced by the prevalence of the East Asian monsoon and the uplift of the Hengduan Mountains (HDM). In summary, our study provides novel insights into the plastome evolution, phylogenetic relationships, taxonomic framework and evolution of genus Sanicula.

DNA barcoding of herbal supplements on the US commercial market associated with the purported treatment of COVID-19.

The COVID-19 pandemic was associated with an increased global use of traditional medicines, including Ayurvedic herbal preparations. Due to their growing demand, their processed nature, and the complexity of the global supply chain, there is an increased risk of adulteration in these products. The objective of this study was to assess the use of DNA barcoding for species identification in herbal supplements on the US market associated with the Ayurvedic treatment of respiratory symptoms. A total of 54 commercial products containing Ayurvedic herbs were tested with four DNA barcoding regions (i.e., rbcL, matK, ITS2, and mini-ITS2) using two composite samples per product. Nine categories of herbs were targeted: amla, ashwagandha, cinnamon, ginger, guduchi, tribulus, tulsi, turmeric, and vacha. At least one species was identified in 64.8% of products and the expected species was detected in 38.9% of products. Undeclared plant species, including other Ayurvedic herbs, rice, and pepper, were detected in 19 products, and fungal species were identified in 12 products. The presence of undeclared plant species may be a result of intentional substitution or contamination during harvest or processing, while fungal DNA was likely associated with the plant material or the growing environment. The greatest sequencing success (42.6-46.3%) was obtained with the matK and rbcL primers. The results of this study indicate that a combination of genetic loci should be used for DNA barcoding of herbal supplements. Due to the limitations of DNA barcoding in identification of these products, future research should incorporate chemical characterization techniques.

Traceability challenges and heavy metal risks in commercial shrimp and prawn

Mislabelling in the global fisheries sector raises concerns about the identity, safety, and sustainability of seafood products. It puts human health at risk when substitute species are contaminated with heavy metals that may cause chronic diseases and cancer. The aim of this work was to analyse mislabelling in shrimps and prawns sold in the Spanish market and possible risks of heavy metal ingestion. Analysis of labels, DNA barcoding for species identification and quantification of heavy metals were performed on 100 market samples, and health risk was calculated from standard indices. More than one half of individuals did not comply with European regulations about labels, principally for the absence of mandatory elements in the label. One third of the analysed shrimps were substitute species (not mentioned on the label), and a 10% did not comply with the legal European limits for heavy metals. The prawns Penaeus indicus and Penaeus latisulcatus from West Indian and Central/East Atlantic waters exhibited the highest heavy metals concentrations. Indices calculated for these two species, and for Pandalus borealis and Parapenaeus longirostris, suggest health risks if consumed daily. If those or other species from these polluted areas were employed as substitutes, mislabelling would encompass health risk.

Detailed integrative taxonomic analysis reveals large-scale species misidentification of barnacles based on DNA barcoding data

Abstract Morphological species identification is the traditional way to identify species. More recently, biodiversity studies have depended on DNA barcoding for species identification. Mismatches between morphological and genetic species identification caused by voucher specimen misidentifications lead to ambiguous species identification. We used barnacles of the genera Amphibalanus and Balanus to investigate this issue. The purpose of this study was to assess the accuracy of the Barcoding of Life database and determine the true species affinity of three inconsistent barnacle barcode index numbers using an integrative taxonomic approach. To this end, we re-identified barcoded voucher specimens, or we identified specimens based on a dichotomous key that we barcoded subsequently. We found that 75% of Barcoding of Life clades representing genetic species showed inconsistent species assignments. One clade (BOLD: AAG0069), containing mostly unidentified Balanus sp. individuals, was morphologically and genetically Balanus balanus (Linneaus, 1758); a second clade (BOLD: AAB1410), containing specimens mostly identified as B. balanus, turned out to be morphologically and genetically Balanus crenatus Bruguière, 1789; and a third clade (BOLD: AAE2482), containing different species of Amphibalanus, was Amphibalanus improvisus (Darwin, 1854). This study showed that morphological species identification and taxonomic expertise can resolve the widespread misidentification in barcoding data. To prevent this problem in the future, morphological taxonomy and molecular species identification need to interact more closely.

DNA barcoding data release for the Phoridae (Insecta, Diptera) of the Halimun-Salak National Park (Java, Indonesia).

Launched in 2015, the large-scale initiative Indonesian Biodiversity Discovery and Information System (IndoBioSys) is a multidisciplinary German-Indonesian collaboration with the main goal of establishing a standardised framework for species discovery and all associated steps. One aspect of the project includes the application of DNA barcoding for species identification and biodiversity assessments. In this framework, we conducted a large-scale assessment of the insect fauna of the Mount Halimun-Salak National Park which is one of the largest tropical rain-forest ecosystems left in West Java. In this study, we present the results of processing 5,034 specimens of Phoridae (scuttle flies) via DNA barcoding. Despite limited sequencing success, we obtained more than 500 clusters using different algorithms (RESL, ASAP, SpeciesIdentifier). Moreover, Chao statistics indicated that we drastically undersampled all trap sites, implying that the true diversity of Phoridae is, in fact, much higher. With this data release, we hope to shed some light on the hidden diversity of this megadiverse group of flies.

Molecular Barcoding: A Tool to Guarantee Correct Seafood Labelling and Quality and Preserve the Conservation of Endangered Species.

The recent increase in international fish trade leads to the need for improving the traceability of fishery products. In relation to this, consistent monitoring of the production chain focusing on technological developments, handling, processing and distribution via global networks is necessary. Molecular barcoding has therefore been suggested as the gold standard in seafood species traceability and labelling. This review describes the DNA barcoding methodology for preventing food fraud and adulteration in fish. In particular, attention has been focused on the application of molecular techniques to determine the identity and authenticity of fish products, to discriminate the presence of different species in processed seafood and to characterize raw materials undergoing food industry processes. In this regard, we herein present a large number of studies performed in different countries, showing the most reliable DNA barcodes for species identification based on both mitochondrial (COI, cytb, 16S rDNA and 12S rDNA) and nuclear genes. Results are discussed considering the advantages and disadvantages of the different techniques in relation to different scientific issues. Special regard has been dedicated to a dual approach referring to both the consumer's health and the conservation of threatened species, with a special focus on the feasibility of the different genetic and genomic approaches in relation to both scientific objectives and permissible costs to obtain reliable traceability.

Phylogenomics and plastome evolution of Indigofera (Fabaceae).

Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera. Here, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae. The chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.

DNA Barcoding of Black Flies (Diptera: Simuliidae) in Slovakia and Its Utility for Species Identification

DNA barcoding based on the cytochrome oxidase I gene is increasingly used in black flies (Diptera: Simuliidae), but extensive data for larger areas are still rare. Slovakia, with well-explored black fly fauna, was chosen to verify the reliability of DNA barcoding for species identification. The DNA barcoding region of the COI gene of 235 individuals of 25 black fly species from Slovakia was sequenced. Among them, 30 sequence clusters with assigned Barcode Index Numbers (BINs) were identified, and 5 of them were recorded for the first time. The average intraspecific genetic divergence was 0–3.24%, whereas the average interspecific divergence was 12.3–17.8%. Based on the barcode sequence, 14 species could be identified unambiguously, and 3 of them (Prosimulium latimucro, Simulium costatum, S. degrangei) are split into two or more barcode clusters. In eleven species, some degree of barcode sharing occurred, often combined with barcode splitting. The results showed hidden diversity as well as cases of shared barcode sequences among the studied species. Further investigation using other molecular markers is necessary due to the overlap of intraspecific and interspecific variability.

Phylogenetic and Morphological Characteristics Reveal Cryptic Speciation in Stingless Bee, Tetragonula laeviceps s.l. Smith 1857 (Hymenoptera; Meliponinae).

Tetragonula laeviceps sensu lato (s.l.) Smith 1857 has the most complicated nomenclatural history among the Tetragonula genera. The objective of this study was to investigate whether T. laeviceps s.l. individuals with worker bees are grouped in the same or nearly the same morphological characteristics and have similar COI haplotype cluster groups. A total of 147 worker bees of T. laeviceps s.l. were collected from six sampling sites in Sabah (RDC, Tuaran, Kota Marudu, Putatan, Kinarut and Faculty of Sustainable Agriculture (FSA)), but only 36 were selected for further studies. These specimens were first classified according to the most obvious morphological characteristics, i.e., hind tibia color, hind basitarsus color and body size. Group identification was based on morphological characteristics important for distinguishing the four groups within T. laeviceps s.l. The four groups of T. laeviceps s.l. had significantly different body trait measurements for the TL (total length), HW (head width), HL (head length), CEL (compound eye length), CEW (compound eye width), FWLT (forewing length, including tegula), FWW (forewing width), FWL (forewing length), ML (mesoscutum length), MW (mesoscutum width), SW (mesoscutellum width), SL (mesoscutellum length), HTL = (hind tibia length), HTW (hind tibia width), HBL (hind basitarsus length) and HBW (hind basitarsus width) (p < 0.001). Body color included HC (head color), CC (clypeus color), ASC (antennae scape color), CFPP (Clypeus and frons plumose pubescence), HTC (hind tibia color), BSC (basitarsus color), SP (leg setae pubescence), SP (Thorax mesoscutellum pubescence), SPL (thorax mesoscutellum pubescence length) and TC (thorax color) (p < 0.05). The most distinctive features of the morphological and morphometric characteristics measured by PCA and LDA biplot that distinguish Group 1 (TL6-1, TL6-2 and TL6-3) from the other groups were the yellowish-brown ASC and the dark brown TC. Group 2 (haplotypes TL2-1, TL2-2 and TL2-3 and TL4-1, TL4-2 and TL4-3) had a dark brown ASC and a black TC, while Group 3 (haplotypes TL11-1, TL11-2 and TL11-3) had a blackish-brown ASC, a black TC and the largest TL, FWW and FWL. As for phylogenetic relationships, 12 out of 36 haplotypes showed clear separation with good bootstrap values (97-100%). The rest of the haplotypes did not show clear differentiation between subclades that belonged together, regardless of their morphology and morphometric characteristics. This suggests that the combination of DNA barcoding for species identification and phylogenetic analysis, as well as traditional methods based on morphological grouping by body size and body color, can be reliably used to determine intraspecific variations within T. laeviceps s.l.

DNA barcoding for species identification and phylogenetic investigation employing five genetic markers of Withania coagulans

DNA barcoding for species identification and phylogenetic investigation employing five genetic markers of Withania coagulans

Newly reported chloroplast genome of Sinosenecio albonervius Y. Liu & Q. E. Yang and comparative analyses with other Sinosenecio species

BackgroundSinosenecio B. Nordenstam (Asteraceae) currently comprises 44 species. To investigate the interspecific relationship, several chloroplast markers, including ndhC-trnV, rpl32-trnL, matK, and rbcL, are used to analyze the phylogeny of Sinosenecio. However, the chloroplast genomes of this genus have not been thoroughly investigated. We sequenced and assembled the Sinosenecio albonervius chloroplast genome for the first time. A detailed comparative analysis was performed in this study using the previously reported chloroplast genomes of three Sinosenecio species.ResultsThe results showed that the chloroplast genomes of four Sinosenecio species exhibit a typical quadripartite structure. There are equal numbers of total genes, protein-coding genes and RNA genes among the annotated genomes. Per genome, 49–56 simple sequence repeats and 99 repeat sequences were identified. Thirty codons were identified as RSCU values greater than 1 in the chloroplast genome of S. albonervius based on 54 protein-coding genes, indicating that they showed biased usage. Among 18 protein-coding genes, 46 potential RNA editing sites were discovered. By comparing these chloroplast genomes' structures, inverted repeat regions and coding regions were more conserved than single-copy and non-coding regions. The junctions among inverted repeat and single-copy regions showed slight difference. Several hot spots of genomic divergence were detected, which can be used as new DNA barcodes for species identification. Phylogenetic analysis of the whole chloroplast genome showed that the four Sinosenecio species have close interspecific relationships.ConclusionsThe complete chloroplast genome of Sinosenecio albonervius was revealed in this study, which included a comparison of Sinosenecio chloroplast genome structure, variation, and phylogenetic analysis for related species. These will help future research on Sinosenecio taxonomy, identification, origin, and evolution to some extent.

INSIGHTS INTO THE EVOLUTION OF THE CHLOROPLAST GENOME AND THE PHYLOGENY OF BEGONIA

Begonia (Begoniaceae) is one of the largest angiosperm genera, comprising more than 2000 species; this makes it ideal as a model to investigate the genomic basis of species radiations. Here we present the results of the first genus-wide comparative study of plastid genome structure, sequence diversity, and phylogenetics of Begoniaceae, in which 44 complete Begoniaceae plastomes, including those of Begonia’s sister group, Hillebrandia, a monotypic genus endemic to Hawai‘i, and 43 species representing 42 sections of Begonia, were assembled. Our results reveal that Begoniaceae plastome size ranges from 167,123 to 170,852 bp, displaying the typical quadripartite structure. Structures of most Begoniaceae plastomes are highly conserved but differ from the plastomes of the majority of angiosperms in having a unique inverted repeat (IR) expansion, from IRa to large single copy (LSC), resulting from a duplicated fragment of the trnH–GUG gene to the trnR–UCU gene. Additionally, comparison between plastomes of Hillebrandia and Begonia shows that the former genus has fewer simple sequence repeats than most Begonia species analysed, suggesting that species of Begonia have more repetitive and dynamic plastomes than those of its sister genus. We also identified six highly variable regions suitable for phylogenetic analysis and as potential DNA barcodes for species identification. Our robust hypothesis of plastome phylogenomic relationships provides new insights into infrageneric classification and highlights potential classification issues in Begonia.

Let’s talk about the (lady)birds and the bees: how insects can whisper a multitude of stories

If you have watched A Bug’s Life, you would have seen that insects come in an assortment of colours, shapes, and sizes. They are the perfect organism that could be used to describe the myriad diversity of all life on earth. These six-legged creatures are one of the most diverse groups of species, accounting for more than 80% of all documented living animals Ødegaard 2008. This huge diversity also makes it extremely time- and labour-intensive to carry out large-scale monitoring of insects. High-throughput sequencing technologies and the use of DNA barcodes for species identification have paved the way for the rapid biomonitoring of insects Hebert et al. 2003. However, millions of insect species are not well-represented in DNA reference databases, making species-level identification challenging for molecular research. Projects such as the Darwin Tree of Life (DToL) aim to cover this gap and generate DNA barcodes for all eukaryotic species found in the UK Blaxter et al. 2022. At the Wellcome Sanger Institute, the BIOSCAN UK for Flying Insects project has two main aims; Documenting the diversity of UK flying insects Discovering insect-cobiont interactions Documenting the diversity of UK flying insects Discovering insect-cobiont interactions To meet these aims, we will be documenting the diversity of one million malaise-caught insects from 100 sites across the UK in the next five years. We will be using a non-destructive DNA extraction technique to preserve insect specimen integrity for museum collections or educational purposes Korlević et al. 2021. COI barcoding will be carried out using ONT and/or PacBio long-read technology to identify each insect specimen. To tease apart insect conbiont interactions, we will carry out mini barcoding using primers targeting microbes, parasites, vertebrates, invertebrates, and plants Fig. 1. Together, this molecular dataset consisting of one million specimens collected over space and time in the next five years will allow us to discover how insects interact with the ecosystem and advance insect biomonitoring research in the UK.

Molecular taxonomy via DNA barcodes for species identification in selected genera of Fabaceae

Fabaceae is an invaluable plant family with considerable ecological and economic importances for example as food sources, bio-fertilizer, and medicinal plants. However, Fabaceae has been overexploited in Indonesia and several species belong to this family are critically endangered. Due to morphological similarity, rapid and accurate identification of Fabaceae species is essential to support its conservation efforts. Nowadays, species identification through DNA barcoding has become an effective taxonomic classification tool. This study was aimed to evaluate the effectiveness of chloroplast markers, matK and rbcL and the combination (matK+rbcL), as DNA barcodes for the identification of seleted genera in Fabaceae. The result showed that matK+rbcL and matK had the highest level of identification (90% and 82.05%) of the investigated genera, respectively. Additionally, matK had the highest mean of interspesific distance (0.134) and intraspecific distance (0.003). The combined barcode matK+rbcL had the highest correct identification rate when comparing the morphological with molecular identification. Furthermore, the best phylogenetic tree was obtained using Neighbor Joining method. Based on the overall performance, matK and matK+rbcL were the best barcodes for the selected genera in this study.

Systematics of Mukdenia and Oresitrophe (Saxifragaceae): Insights from genome skimming data

AbstractOresitrophe and Mukdenia (Saxifragaceae) are epilithic sister genera used in traditional Chinese medicine. The taxonomy of Mukdenia, especially of M. acanthifolia, has been controversial. To address this, we produced plastid and mitochondrial data using genome skimming for Mukdenia acanthifolia and Mukdenia rossii, including three individuals of each species. We assembled complete plastomes, mitochondrial CDS and nuclear ribosomal ETS/ITS sequences using these data. Comparative analysis shows that the plastomes of Mukdenia and Oresitrophe are relatively conservative in terms of genome size, structure, gene content, RNA editing sites and codon usage. Five plastid regions that represent hotspots of change (trnH‐psbA, psbC‐trnS, trnM‐atpE, petA‐psbJ and ccsA‐ndhD) are identified within Mukdenia, and six regions (trnH‐psbA, petN‐psbM, trnM‐atpE, rps16‐trnQ, ycf1 and ndhF) contain a higher number of species‐specific parsimony‐informative sites that may serve as potential DNA barcodes for species identification. To infer phylogenetic relationships between Mukdenia and Oresitrophe, we combined our data with published data based on three different datasets. The monophyly of each species (Oresitrophe rupifraga, M. acanthifolia and M. rossii) and the inferred topology ((M. rossii, M. acanthifolia), O. rupifraga) are well supported in trees reconstructed using the complete plastome sequences, but M. acanthifolia and M. rossii did not form a separate clade in the trees based on ETS + ITS data, while the mitochondrial CDS trees are not well‐resolved. We found low recovery of genes in the Angiosperms353 target enrichment panel from our unenriched genome skimming data. Hybridization or incomplete lineage sorting may be the cause of discordance between trees reconstructed from organellar and nuclear data. Considering its morphological distinctiveness and our molecular phylogenetic results, we strongly recommend that M. acanthifolia be treated as a distinct species.

The complete plastomes of seven Peucedanum plants: comparative and phylogenetic analyses for the Peucedanum genus

BackgroundThe Peucedanum genus is the backbone member of Apiaceae, with many economically and medically important plants. Although the previous studies on Peucedanum provide us with a good research basis, there are still unclear phylogenetic relationships and many taxonomic problems in Peucedanum, and a robust phylogenetic framework of this genus still has not been obtained, which severely hampers the improvement and revision of taxonomic system for this genus. The plastid genomes possessing more variable characters have potential for reconstructing a robust phylogeny in plants.ResultsIn the current study, we newly sequenced and assembled seven Peucedanum plastid genomes. Together with five previously published plastid genomes of Peucedanum, we performed a comprehensively comparative analyses for this genus. Twelve Peucedanum plastomes were similar in terms of genome structure, codon bias, RNA editing sites, and SSRs, but varied in genome size, gene content and arrangement, and border of SC/IR. Fifteen mutation hotspot regions were identified among plastid genomes that can serve as candidate DNA barcodes for species identification in Peucedanum. Our phylogenetic analyses based on plastid genomes generated a phylogeny with high supports and resolutions for Peucedanum that robustly supported the non-monophyly of genus Peucedanum.ConclusionThe plastid genomes of Peucedanum showed both conservation and diversity. The plastid genome data were efficient and powerful for improving the supports and resolutions of phylogeny for the complex Peucedanum genus. In summary, our study provides new sights into the plastid genome evolution, taxonomy, and phylogeny for Peucedanum species.

Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships.

Hoya is a genus in Apocynaceae-Asclepiadoideae, known for its showy wax flowers, making it a popular ornamental plant. However, phylogenetic relationships among most Hoya species are not yet fully resolved. In this study, we sequenced 31 plastomes of Hoya group species using genome skimming data and carried out multiple analyses to understand genome variation to resolve the phylogenetic positions of some newly sequenced Chinese endemic species. We also screened possible hotspots, trnT-trnL-trnF, psba-trnH, and trnG-UCC, ndhF, ycf1, matK, rps16, and accD genes that could be used as molecular markers for DNA barcoding and species identification. Using maximum likelihood (ML) and Bayesian Inference (BI), a species phylogeny was constructed. The newly assembled plastomes genomes showed the quasi-tripartite structure characteristic for Hoya and Dischidia with a reduced small single copy (SSC) and extremely enlarged inverted repeats (IR). The lengths ranged from 175,404 bp in Hoya lacunosa to 179,069 bp in H. ariadna. The large single copy (LSC) regions ranged from 80,795 bp (Hoya liangii) to 92,072 bp (Hoya_sp2_ZCF6006). The massively expanded IR regions were relatively conserved in length, with the small single-copy region reduced to a single gene, ndhF. We identified 235 long dispersed repeats (LDRs) and ten highly divergent hotspots in the 31 Hoya plastomes, which can be used as DNA barcodes for species identification. The phylogeny supports Clemensiella as a distinct genus. Hoya ignorata is resolved as a relative to Clade VI species. This study discloses the advantages of using Plastome genome data to study phylogenetic relationships.

The Ocean Genome Legacy: A Genomic Resource Repository for Marine Life.

The Ocean Genome Legacy: A Genomic Resource Repository for Marine Life.

DNA barcoding of Naididae (Annelida, Oligochaeta), based on cytochrome C oxidase gene and ITS2 region in China.

Exploring the effectiveness of DNA barcoding in species identification is a prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaetes could serve as excellent indicators in aquatic monitoring programmes. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial cytochrome C oxidase (COI) gene of 83 specimens belonging to 40 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification, except for Tubifextubifex and Lumbriculusvariegatus. All species were successfully distinguished in the phylogenetic tree, based on the ITS2 region, which was coincident with the morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even for other aquatic oligochaetes.